Merge branch 'workflows' of https://github.com/shapiromatron/hawc int…

…o workflows

frontend/shared/utils/HAWCUtils.js

@@ -302,7 +302,12 @@ class HAWCUtils {
             handleChange = () => {
                 const selector = `#detail-${$selectEl.val()}`,
                     clone = $insertItems.find(selector).clone();
-                $insertEl.fadeOut(() => $insertEl.html(clone).fadeIn());
+                $insertEl.fadeOut(() =>
+                    $insertEl
+                        .html(clone)
+                        .trigger("select:change")
+                        .fadeIn()
+                );
             };
         $selectEl.on("change", handleChange).trigger("change");
     }

hawc/apps/summary/constants.py

@@ -28,6 +28,26 @@ class VisualType(models.IntegerChoices):
     PLOTLY = 7, "plotly"
 
 
+VISUAL_EVIDENCE_CHOICES = {
+    VisualType.BIOASSAY_AGGREGATION: {StudyType.BIOASSAY},
+    VisualType.BIOASSAY_CROSSVIEW: {StudyType.BIOASSAY},
+    VisualType.ROB_HEATMAP: {StudyType.BIOASSAY, StudyType.EPI, StudyType.IN_VITRO},
+    VisualType.ROB_BARCHART: {StudyType.BIOASSAY, StudyType.EPI, StudyType.IN_VITRO},
+    VisualType.LITERATURE_TAGTREE: {StudyType.OTHER},
+    VisualType.EXTERNAL_SITE: {StudyType.OTHER},
+    VisualType.EXPLORE_HEATMAP: {StudyType.OTHER},
+    VisualType.PLOTLY: {StudyType.OTHER},
+}
+
+
+def get_default_evidence_type(visual_type: VisualType) -> StudyType:
+    """Return StudyType for visual if only one option exists, otherwise raise ValueError."""
+    choices = VISUAL_EVIDENCE_CHOICES[visual_type]
+    if len(choices) > 1:
+        raise ValueError(f"No default evidence type for visual {visual_type}; multiple exist.")
+    return next(iter(choices))
+
+
 class SortOrder(models.TextChoices):
     SC = "short_citation", "Short Citation"
     OC = "overall_confidence", "Final Study Confidence"

hawc/apps/summary/forms.py

@@ -128,11 +128,12 @@ def get_cancel_url(self):
 class VisualForm(forms.ModelForm):
     class Meta:
         model = models.Visual
-        exclude = ("assessment", "visual_type", "prefilters")
+        exclude = ("assessment", "visual_type", "evidence_type", "prefilters")
 
     def __init__(self, *args, **kwargs):
         assessment = kwargs.pop("parent", None)
         visual_type = kwargs.pop("visual_type", None)
+        evidence_type = kwargs.pop("evidence_type", None)
         super().__init__(*args, **kwargs)
         if "settings" in self.fields:
             self.fields["settings"].widget.attrs["rows"] = 2
@@ -149,6 +150,8 @@ def __init__(self, *args, **kwargs):
             constants.VisualType.PLOTLY,
         ]:
             self.fields["sort_order"].widget = forms.HiddenInput()
+        if self.instance.id is None:
+            self.instance.evidence_type = evidence_type
 
     def setHelper(self):
         for fld in list(self.fields.keys()):
@@ -191,6 +194,14 @@ def clean_caption(self):
         validators.validate_hyperlinks(caption)
         return validators.clean_html(caption)
 
+    def clean_evidence_type(self):
+        visual_type = self.cleaned_data["visual_type"]
+        evidence_type = self.cleaned_data["evidence_type"]
+        if evidence_type not in constants.VISUAL_EVIDENCE_CHOICES[visual_type]:
+            raise forms.ValidationError(
+                f"Invalid evidence type {evidence_type} for visual {visual_type}."
+            )
+
 
 class VisualModelChoiceField(forms.ModelChoiceField):
     def label_from_instance(self, obj):
@@ -239,7 +250,15 @@ def __init__(self, *args, **kwargs):
 
     class Meta:
         model = models.Visual
-        exclude = ("assessment", "visual_type", "settings", "prefilters", "studies", "sort_order")
+        exclude = (
+            "assessment",
+            "visual_type",
+            "evidence_type",
+            "settings",
+            "prefilters",
+            "studies",
+            "sort_order",
+        )
 
 
 class CrossviewForm(VisualForm):
@@ -257,17 +276,17 @@ def __init__(self, *args, **kwargs):
         self.fields["dose_units"].queryset = DoseUnits.objects.get_animal_units(
             self.instance.assessment
         )
-        self.prefilter_cls = prefilters.VisualTypePrefilter.from_visual_type(
-            constants.VisualType.BIOASSAY_CROSSVIEW
-        ).value
+        self.prefilter_cls = prefilters.get_prefilter_cls(
+            self.instance.visual_type, self.instance.evidence_type, self.instance.assessment
+        )
         self.fields["prefilters"] = DynamicFormField(
             prefix="prefilters", form_class=self._get_prefilter_form, label=""
         )
         self.helper = self.setHelper()
 
     class Meta:
         model = models.Visual
-        exclude = ("assessment", "visual_type", "endpoints", "studies")
+        exclude = ("assessment", "visual_type", "evidence_type", "endpoints", "studies")
 
 
 class RoBForm(VisualForm):
@@ -282,17 +301,17 @@ def _get_prefilter_form(self, data, **form_kwargs):
 
     def __init__(self, *args, **kwargs):
         super().__init__(*args, **kwargs)
-        self.prefilter_cls = prefilters.VisualTypePrefilter.from_visual_type(
-            constants.VisualType.ROB_BARCHART
-        ).value
+        self.prefilter_cls = prefilters.get_prefilter_cls(
+            self.instance.visual_type, self.instance.evidence_type, self.instance.assessment
+        )
         self.fields["prefilters"] = DynamicFormField(
             prefix="prefilters", form_class=self._get_prefilter_form, label=""
         )
         self.helper = self.setHelper()
 
     class Meta:
         model = models.Visual
-        exclude = ("assessment", "visual_type", "dose_units", "endpoints")
+        exclude = ("assessment", "visual_type", "evidence_type", "dose_units", "endpoints")
 
 
 class TagtreeForm(VisualForm):
@@ -703,9 +722,9 @@ def __init__(self, *args, **kwargs):
         if self.instance.id is None:
             self.instance.evidence_type = evidence_type
 
-        self.prefilter_cls = prefilters.StudyTypePrefilter.from_study_type(
-            self.instance.evidence_type, self.instance.assessment
-        ).value
+        self.prefilter_cls = prefilters.get_prefilter_cls(
+            None, self.instance.evidence_type, self.instance.assessment
+        )
         self.fields["prefilters"] = DynamicFormField(
             prefix="prefilters", form_class=self._get_prefilter_form, label=""
         )

hawc/apps/summary/migrations/0045_datapivotquery_prefilters_json.py

@@ -4,12 +4,12 @@
 
 from django.db import migrations, models
 
-from hawc.apps.summary.prefilters import StudyTypePrefilter
+from hawc.apps.summary.prefilters import EndpointPrefilter, get_prefilter_cls
 
 logger = logging.getLogger(__name__)
 
 mapping = {
-    StudyTypePrefilter.BIOASSAY: {
+    EndpointPrefilter.BIOASSAY.value: {
         "published_only": "animal_group__experiment__study__published",
         "studies": "animal_group__experiment__study__in",
         "systems": "system__in",
@@ -18,30 +18,30 @@
         "effect_subtypes": "effect_subtype__in",
         "effect_tags": "effects__in",
     },
-    StudyTypePrefilter.EPIV1: {
+    EndpointPrefilter.EPIV1.value: {
         "published_only": "study_population__study__published",
         "studies": "study_population__study__in",
         "systems": "system__in",
         "effects": "effect__in",
         "effect_tags": "effects__in",
     },
-    StudyTypePrefilter.EPIV2: {
+    EndpointPrefilter.EPIV2.value: {
         "published_only": "design__study__published",
         "studies": "design__study__in",
     },
-    StudyTypePrefilter.EPI_META: {
+    EndpointPrefilter.EPI_META.value: {
         "published_only": "protocol__study__published",
         "studies": "protocol__study__in",
     },
-    StudyTypePrefilter.IN_VITRO: {
+    EndpointPrefilter.IN_VITRO.value: {
         "published_only": "experiment__study__published",
         "studies": "experiment__study__in",
         "categories": "category__in",
         "chemicals": "chemical__name__in",
         "effects": "effect__in",
         "effect_tags": "effects__in",
     },
-    StudyTypePrefilter.ECO: {
+    EndpointPrefilter.ECO.value: {
         "published_only": "design__study__published",
         "studies": "design__study__in",
     },
@@ -56,7 +56,7 @@ def prefilters_dict(apps, schema_editor):
         data = json.loads(obj.prefilters)
         if not data:
             continue
-        key_map = mapping[StudyTypePrefilter.from_study_type(obj.evidence_type, obj.assessment)]
+        key_map = mapping[get_prefilter_cls(None, obj.evidence_type, obj.assessment)]
         key_map = {v: k for k, v in key_map.items()}
         data = {key_map[k]: v for k, v in data.items() if v}
         obj.temp = data
@@ -70,7 +70,7 @@ def reverse_prefilters_dict(apps, schema_editor):
     for obj in objs:
         if not obj.temp:
             continue
-        key_map = mapping[StudyTypePrefilter.from_study_type(obj.evidence_type, obj.assessment)]
+        key_map = mapping[get_prefilter_cls(None, obj.evidence_type, obj.assessment)]
         data = {key_map[k]: v for k, v in obj.temp.items()}
         obj.prefilters = json.dumps(data)
     DataPivotQuery.objects.bulk_update(objs, ["prefilters"])

hawc/apps/summary/migrations/0046_visual_prefilters_json.py

@@ -3,36 +3,14 @@
 
 from django.db import migrations, models
 
-from hawc.apps.summary.prefilters import VisualTypePrefilter
-
-mapping = {
-    VisualTypePrefilter.BIOASSAY_CROSSVIEW: {
-        "published_only": "animal_group__experiment__study__published",
-        "studies": "animal_group__experiment__study__in",
-        "systems": "system__in",
-        "organs": "organ__in",
-        "effects": "effect__in",
-        "effect_subtypes": "effect_subtype__in",
-        "effect_tags": "effects__in",
-    },
-    VisualTypePrefilter.ROB_HEATMAP: {
-        "published_only": "animal_group__experiment__study__published",
-        "studies": "animal_group__experiment__study__in",
-        "systems": "system__in",
-        "organs": "organ__in",
-        "effects": "effect__in",
-        "effect_subtypes": "effect_subtype__in",
-        "effect_tags": "effects__in",
-    },
-    VisualTypePrefilter.ROB_BARCHART: {
-        "published_only": "animal_group__experiment__study__published",
-        "studies": "animal_group__experiment__study__in",
-        "systems": "system__in",
-        "organs": "organ__in",
-        "effects": "effect__in",
-        "effect_subtypes": "effect_subtype__in",
-        "effect_tags": "effects__in",
-    },
+key_map = {
+    "published_only": "animal_group__experiment__study__published",
+    "studies": "animal_group__experiment__study__in",
+    "systems": "system__in",
+    "organs": "organ__in",
+    "effects": "effect__in",
+    "effect_subtypes": "effect_subtype__in",
+    "effect_tags": "effects__in",
 }
 
 
@@ -44,9 +22,8 @@ def prefilters_dict(apps, schema_editor):
         data = json.loads(obj.prefilters)
         if not data:
             continue
-        key_map = mapping[VisualTypePrefilter.from_visual_type(obj.visual_type)]
-        key_map = {v: k for k, v in key_map.items()}
-        data = {key_map[k]: v for k, v in data.items() if v}
+        reverse_key_map = {v: k for k, v in key_map.items()}
+        data = {reverse_key_map[k]: v for k, v in data.items() if v}
         obj.temp = data
     Visual.objects.bulk_update(objs, ["temp"])
 
@@ -58,7 +35,6 @@ def reverse_prefilters_dict(apps, schema_editor):
     for obj in objs:
         if not obj.temp:
             continue
-        key_map = mapping[VisualTypePrefilter.from_visual_type(obj.visual_type)]
         data = {key_map[k]: v for k, v in obj.temp.items()}
         obj.prefilters = json.dumps(data)
     Visual.objects.bulk_update(objs, ["prefilters"])

hawc/apps/summary/migrations/0051_visual_evidence_type.py

@@ -0,0 +1,61 @@
+# Generated by Django 4.2.3 on 2023-10-24 16:32
+
+from django.db import migrations, models
+
+from hawc.apps.summary.constants import get_default_evidence_type
+
+
+def set_defaults(apps, schema_editor):
+    Visual = apps.get_model("summary", "Visual")
+    objs = Visual.objects.all()
+    updated_objs = []
+    for obj in objs:
+        # if theres a default evidence_type, use it
+        try:
+            evidence_type = get_default_evidence_type(obj.visual_type)
+            obj.evidence_type = evidence_type
+        # otherwise assume bioassay remains the default
+        except ValueError:
+            pass
+        if obj.evidence_type != 0:
+            updated_objs.append(obj)
+    Visual.objects.bulk_update(updated_objs, ["evidence_type"])
+
+
+class Migration(migrations.Migration):
+    dependencies = [
+        ("summary", "0050_heatmap_counts"),
+    ]
+
+    operations = [
+        migrations.AddField(
+            model_name="visual",
+            name="evidence_type",
+            field=models.PositiveSmallIntegerField(
+                choices=[
+                    (0, "Animal Bioassay"),
+                    (1, "Epidemiology"),
+                    (4, "Epidemiology meta-analysis/pooled analysis"),
+                    (2, "In vitro"),
+                    (5, "Ecology"),
+                    (3, "Other"),
+                ],
+                default=0,
+            ),
+        ),
+        migrations.RunPython(set_defaults, migrations.RunPython.noop),
+        migrations.AlterField(
+            model_name="visual",
+            name="evidence_type",
+            field=models.PositiveSmallIntegerField(
+                choices=[
+                    (0, "Animal Bioassay"),
+                    (1, "Epidemiology"),
+                    (4, "Epidemiology meta-analysis/pooled analysis"),
+                    (2, "In vitro"),
+                    (5, "Ecology"),
+                    (3, "Other"),
+                ]
+            ),
+        ),
+    ]